Bacillus Pumilus RTMG: Difference between revisions

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<i>Genus species:</i> <i>Bacillus pumilus</i>
Genus species: <i><b>Bacillus pumilus</b></i>


==Habitat Information ==
==Habitat Information ==
Latitude: 30.26 degrees Longitude: 97.69 degrees
Latitude: 30.398974 degrees Longitude: -97.704909 degrees


It was a clear day with a temperature of 64 degrees in the area of Govalle, East Austin on January 25th 2018. A ziplock bag was used to collect the soil from the area mostly from the surface about one inch deep. The location of the soil sample chosen was in a neighborhood field often frequented by dogs. Rainfall was 0.0" and the pressure was 35.35". The description of the location was mostly Bergstrom soils and urban land. 0-2% slopes and rarely flooded.
It was a clear day with a temperature of 65 F in the area of central Austin on January 25th 2018. A zip lock bag was used to collect the soil from the area mostly from the surface about a half inch deep. The location of the soil sample was taken from an area close to residential buildings underneath a tree. Rainfall was 0.0" and the pressure was 30.13 inHg. The description of the location was mostly Austin silty clay and urban land. 2-5% slopes and eroded.


==Description and Significance==
Generally this species is found in soil. [2]
Describe the appearance (colonial and cellular), possible antimicrobial activity etc. of the organism, and why the organism might be significant.






Cellular: gram negative aerobic
Description:
Describe the appearance (colonial and cellular), possible antimicrobial activity etc. of the organism.


Colonial:
 
 
Cellular: Gram positive
 
Colonial: rod-shape
 
Aerobic
 
Spore-Forming


==Genome Structure==
==Genome Structure==
Describe the size and content of the genome.  How many chromosomes?  Circular or linear?  Other interesting features?  What is known about its sequence? Include S Ribosomal sequence that you obtained from PCR and sequencing here.
Describe the size and content of the genome.  How many chromosomes?  Circular or linear?  Other interesting features?  What is known about its sequence? Include S Ribosomal sequence that you obtained from PCR and sequencing here.


ED2-Reverse_B05.ab1
>RM1_4-16S-rRNA-SeqF_D09.ab1
ACCGTCCTCCCGAAGGTTAGACTAGCTACTTCTGGTGCAACCCACTCCCATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGA
 
ACGTATTCACCGCGACATTCTGATTCGCGATTACTAGCGATTCCGACTTCACGCAGTCGAGTTGCAGACTGCGATCCGGACTACG
ATTATTGGGCGTANGGGCTCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACC
ATCGGTTTTATGGGATTAGCTCCACCTCGCGGCTTGGCAACCCTTTGTACCGACCATTGTAGCACGTGTGTAGCCCAGGCCGTA
GGGGAGGGTCATTGGAAACTGGGAAACTTGAGTGCAGAAGAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGA
AGGGCCATGATGACTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGCAGTCTCCTTAGAGTGCCCACCATTACGTGCTG
GATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACA
GTAACTAAGGACAAGGGTTGCGCTCGTTACGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCAGCACCTG TCTCAATGTTCCCGAAGGCACCAATCCATCTCTGGAAAGTTCATTGGATGTCAAGGCCTGGTAAGGTTCTTCGCGTTGCTTCGAA
GGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCT
TTAAACCACATGCTCCACCGCTTGTGCGGGCCCCCGTCAATTCATTTGAGTTTTAACCTTGCGGCCGTACTCCCCAGGCGGTCA
AACGCATTAAGCACTCCGCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGT
ACTTAATGCGTTAGCTGCGCCACTAAGAGCTCAAGGCTCCCAACGGCTAGTTGACATCGTTTACGGCGTGGACTACCAGGGTAT
GGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCTCTGACAACCCTAGAGATAGGGCT
CTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTA
TTCCCTTCGGGGACAGAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAAC
TATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCTCGCCAGTTTTGGATGCAGTTCCCAGGT
GAGCGCAACCCTTGATCTTAGTTGCCAGCATTTAGTTGGGCACTCTAAGGTGACTGCCGGTGACAAACCGGAGGAAGGTG
TGAGCCCGGGGATTTCACATCCAACTTAACGAACCACCTACGCGCGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCTC
GGGATGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGACAGAACAAAGGGCTGCGAGAC
TGTATTACCGCG
CGCAAGGTTTAGCCAATCCCATAAATCTGTTCTCAGTTCGGATCGCAGTCTGCAACTCGACTGCGTGAAGCTGGAATCGC
TAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAGAGTTTGT
AACACCCGAAGTCGGTGAGGTAACCTTTATGGAGCCAGCCGCCGAA


==Cell Structure, Metabolism and Life Cycle==
==Cell Structure, Metabolism and Life Cycle==
Interesting features of cell structure; how it gains energy; what important molecules it produces.
Interesting features of cell structure; how it gains energy; what important molecules it produces.


Commonly found in soil and water and it is sprayed on crops to prevent fungal pests such as molds and mildews. Used in nurseries, landscapes, and greenhouses. 
This species is generally non-pathogenic although it as been seen in some cases of food poisoning. It is used a probiotic preparation in the treatment of intestinal disorders that fight against fungal infections.
B. subtilis is produces Vit. B12, enzymes, and bacitracin. Their ability to produce antibiotics during sporulation has been helpful for western medicine.
The biofilm communities has a mutualistic (both benefiting) interaction with plant rhizome systems. [1]


==Physiology and Pathogenesis==
==Physiology and Pathogenesis==
<b>BIOCHEMICAL TEST RESULTS</b>
<b>BIOCHEMICAL TEST RESULTS</b>
*<b>Phenol Red Broth Tests:</b> <i>Glucose:</i> positive; <i>Lactose:</i> negative; <i>Sucrose:</i> negative
*<b>Phenol Red Broth Tests:</b> <i>Glucose:</i> positive; <i>Lactose:</i> negative; <i>Sucrose:</i> posititve
*<b>Starch Hydrolysis Test:</b> negative
*<b>Starch Hydrolysis Test:</b> positive
*<b>Casein Hydrolysis Test:</b> negative
*<b>Casein Hydrolysis Test:</b> positive
*<b>Gelatin Hydrolysis Test:</b> positive
*<b>Gelatin Hydrolysis Test:</b> positive
*<b>DNA Hydrolysis Test:</b> slight positive
*<b>DNA Hydrolysis Test:</b> negative
*<b>Lipid Hydrolysis Test:</b> positive
*<b>Lipid Hydrolysis Test:</b> positive
*<b>Methyl Red Test:</b> negative
*<b>Methyl Red Test:</b> negative
*<b>Voges Proskauer Test:</b> negative
*<b>Voges Proskauer Test:</b> positive
*<b>Citrate Test:</b> positive
*<b>Citrate Test:</b> positive
*<b>SIM Tests:</b> negative for all
*<b>SIM Tests:</b> negative for all
*<b>Nitrate Reduction:</b> negative
*<b>Nitrate Reduction:</b> negative
*<b>Urea Hydrolysis:</b> negative
*<b>Urea Hydrolysis:</b> positive
*<b>Triple Sugar Iron Agar:</b> negative for all
*<b>Triple Sugar Iron Agar:</b> negative for all
*<b>Oxidase Test:</b> negative
*<b>Oxidase Test:</b> positive
*<b>Eosin Methylene Blue Agar (EMB) Test:</b> positive
*<b>Eosin Methylene Blue Agar (EMB) Test:</b> negative
*<b>Hektoen Enteric Agar (HE) Test:</b> negative
*<b>Hektoen Enteric Agar (HE) Test:</b> negative
*<b>MacConkey Agar Test:</b> negative
*<b>MacConkey Agar Test:</b> negative
*<b>Decarboxylation Tests:</b> <i>Arginine:</i> no change; <i>Lysine:</i> negative; <i>Orinithine:</i> negative
*<b>Decarboxylation Tests:</b> <i>Arginine:</i> negative; <i>Lysine:</i> negative; <i>Orinithine:</i> negative
*<b> Phenylalanine Deaminase Test:</b> negative
*<b> Phenylalanine Deaminase Test:</b> negative
*<b> Catalase Test:</b> negative
*<b> Catalase Test:</b> positive
*<b> Blood Agar Test:</b> slight positive
*<b> Blood Agar Test:</b> Beta - Complete Breakdown
*<b>Mannitol Salt Agar (MSA) Test:</b> negative
*<b>Mannitol Salt Agar (MSA) Test:</b> negative
*<b>Phenylethyl Alcohol Agar (PEA) Test:</b> negative
*<b>Phenylethyl Alcohol Agar (PEA) Test:</b> Positive
*<b>Bacitracin/Optochin Susceptibility Test:</b> <i>Bacitracin:</i> resistant; <i>Optochin:</i> resistant
*<b>Bacitracin/Optochin Susceptibility Test:</b> <i>Bacitracin:</i> resistant; <i>Optochin:</i> resistant
*<b>Bile Esculin Test: </b> negative
*<b>Bile Esculin Test: </b> positive
*<b>6.5% Salt Tolerance Test: </b>slight positive
*<b>6.5% Salt Tolerance Test: </b>negative
 
==References==


1. United States. National Center for Biotechnology Information. N.p., n.d. Bacillus pumilus: A ubiquitous soil organism. Web. 29 April 2016.  http://www.ncbi.nlm.nih.gov/genome/?term=bacillus%20pumilus


==References==
2. Bacillus pumilus SAFR-032. N.p., n.d. Web. 27 April 2016. http://www.genome.jp/kegg-bin/show_organism?org=bpu
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]
 
3. From, C., Hormazabal, V., and Granum, P. “Food poisoning associated with pumilacidin-producing Bacillus pumilus in rice”. International Journal of Food Microbiology. 2007. Volume 115. p. 319-324.


https://www.ncbi.nlm.nih.gov/pubmed/25410940, "Pseudomonas granadensis sp. nov., a new bacterial species isolated from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain". PubMed.gov. Epub 2014 Nov 19.
4. Tena, D., Martinez-Torres, J., Perez-Pomata, M., Saez-Nieto, J., Rubio, V., and Bisquert, J. “Cutaneous infection due to Bacillus pumilus: Report of 3 cases”. Clinical Infectious Diseases. 2007. Volume 44. P. e40-2.


==Author==
==Author==
Page authored by Diane Marques and Emma Riegle, students of Prof. Kristine Hollingsworth at Austin Community College.
Page authored by Maddy Gregory, students of Prof. Kristine Hollingsworth at Austin Community College.


<!-- Do not remove this line-->[[Category:Pages edited by students of Kristine Hollingsworth at Austin Community College]]
<!-- Do not remove this line-->[[Category:Pages edited by students of Kristine Hollingsworth at Austin Community College]]

Latest revision as of 19:50, 11 August 2019

This student page has not been curated.

Classification

Domain: Bacteria

Phylum: Firmicutes

Class: Bacilli

Order: Bacillales

Family: Bacillaceae

Genus: Bacillus

Other Names:

Species

NCBI: Taxonomy

Genus species: Bacillus pumilus

Habitat Information

Latitude: 30.398974 degrees Longitude: -97.704909 degrees

It was a clear day with a temperature of 65 F in the area of central Austin on January 25th 2018. A zip lock bag was used to collect the soil from the area mostly from the surface about a half inch deep. The location of the soil sample was taken from an area close to residential buildings underneath a tree. Rainfall was 0.0" and the pressure was 30.13 inHg. The description of the location was mostly Austin silty clay and urban land. 2-5% slopes and eroded.

Generally this species is found in soil. [2]


Description: Describe the appearance (colonial and cellular), possible antimicrobial activity etc. of the organism.


Cellular: Gram positive

Colonial: rod-shape

Aerobic

Spore-Forming

Genome Structure

Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence? Include S Ribosomal sequence that you obtained from PCR and sequencing here.

>RM1_4-16S-rRNA-SeqF_D09.ab1

ATTATTGGGCGTANGGGCTCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACC GGGGAGGGTCATTGGAAACTGGGAAACTTGAGTGCAGAAGAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGA GATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACA GGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCT AACGCATTAAGCACTCCGCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGT GGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCTCTGACAACCCTAGAGATAGGGCT TTCCCTTCGGGGACAGAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAAC GAGCGCAACCCTTGATCTTAGTTGCCAGCATTTAGTTGGGCACTCTAAGGTGACTGCCGGTGACAAACCGGAGGAAGGTG GGGATGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGACAGAACAAAGGGCTGCGAGAC CGCAAGGTTTAGCCAATCCCATAAATCTGTTCTCAGTTCGGATCGCAGTCTGCAACTCGACTGCGTGAAGCTGGAATCGC TAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAGAGTTTGT AACACCCGAAGTCGGTGAGGTAACCTTTATGGAGCCAGCCGCCGAA

Cell Structure, Metabolism and Life Cycle

Interesting features of cell structure; how it gains energy; what important molecules it produces.

Commonly found in soil and water and it is sprayed on crops to prevent fungal pests such as molds and mildews. Used in nurseries, landscapes, and greenhouses.

This species is generally non-pathogenic although it as been seen in some cases of food poisoning. It is used a probiotic preparation in the treatment of intestinal disorders that fight against fungal infections.

B. subtilis is produces Vit. B12, enzymes, and bacitracin. Their ability to produce antibiotics during sporulation has been helpful for western medicine.

The biofilm communities has a mutualistic (both benefiting) interaction with plant rhizome systems. [1]

Physiology and Pathogenesis

BIOCHEMICAL TEST RESULTS

  • Phenol Red Broth Tests: Glucose: positive; Lactose: negative; Sucrose: posititve
  • Starch Hydrolysis Test: positive
  • Casein Hydrolysis Test: positive
  • Gelatin Hydrolysis Test: positive
  • DNA Hydrolysis Test: negative
  • Lipid Hydrolysis Test: positive
  • Methyl Red Test: negative
  • Voges Proskauer Test: positive
  • Citrate Test: positive
  • SIM Tests: negative for all
  • Nitrate Reduction: negative
  • Urea Hydrolysis: positive
  • Triple Sugar Iron Agar: negative for all
  • Oxidase Test: positive
  • Eosin Methylene Blue Agar (EMB) Test: negative
  • Hektoen Enteric Agar (HE) Test: negative
  • MacConkey Agar Test: negative
  • Decarboxylation Tests: Arginine: negative; Lysine: negative; Orinithine: negative
  • Phenylalanine Deaminase Test: negative
  • Catalase Test: positive
  • Blood Agar Test: Beta - Complete Breakdown
  • Mannitol Salt Agar (MSA) Test: negative
  • Phenylethyl Alcohol Agar (PEA) Test: Positive
  • Bacitracin/Optochin Susceptibility Test: Bacitracin: resistant; Optochin: resistant
  • Bile Esculin Test: positive
  • 6.5% Salt Tolerance Test: negative

References

1. United States. National Center for Biotechnology Information. N.p., n.d. Bacillus pumilus: A ubiquitous soil organism. Web. 29 April 2016. http://www.ncbi.nlm.nih.gov/genome/?term=bacillus%20pumilus

2. Bacillus pumilus SAFR-032. N.p., n.d. Web. 27 April 2016. http://www.genome.jp/kegg-bin/show_organism?org=bpu

3. From, C., Hormazabal, V., and Granum, P. “Food poisoning associated with pumilacidin-producing Bacillus pumilus in rice”. International Journal of Food Microbiology. 2007. Volume 115. p. 319-324.

4. Tena, D., Martinez-Torres, J., Perez-Pomata, M., Saez-Nieto, J., Rubio, V., and Bisquert, J. “Cutaneous infection due to Bacillus pumilus: Report of 3 cases”. Clinical Infectious Diseases. 2007. Volume 44. P. e40-2.

Author

Page authored by Maddy Gregory, students of Prof. Kristine Hollingsworth at Austin Community College.

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